They did have Jack and Sally at MK during the Halloween party when we went. We stumbled across them by town hall when my wife had to hit the restrooms.
In downtown disney they have a christmas store and for the past several years the last section of the store was dedicated to NMBC merch. I got some great stuff there in the past, however this past time we went it was rather barren looking and the CM stated they were going to remove the section and just make it straight christmas decor all the way through.
I believe there is a villians store at Hollywood Studios that carries some NMBC stuff (as the store in general carries Disney's "darker" merch).
Unfortunately, beyond all that, unless your at MK during the Halloween parties, it seems there isn't much of a Jack presence at all in the parks.